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The Genomic Organization of Plant Pathogenicity in Fusarium Species Martijn Rep1 and H Corby Kistler2

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The Genomic Organization of Plant Pathogenicity in Fusarium Species Martijn Rep1 and H Corby Kistler2 Available online at www.sciencedirect.com The genomic organization of plant pathogenicity in Fusarium species Martijn Rep1 and H Corby Kistler2 Comparative genomics is a powerful tool to infer the molecular cation and genetic transmission. We here highlight recent basis of fungal pathogenicity and its evolution by identifying insights into the evolution of disease-causing ability differences in gene content and genomic organization between among plant pathogenic fungi, focusing on the compara- fungi with different hosts or modes of infection. Through tive genomic analysis of Fusarium species with additional comparative analysis, pathogenicity-related chromosomes reference to other fungi. have been identified in Fusarium oxysporum and Fusarium solani that contain genes for host-specific virulence. Lateral Comparative genomics transfer of pathogenicity chromosomes, inferred from genomic In 2007 the Broad Institute released its first Fusarium data, now has been experimentally confirmed. Likewise, comparativegenomicswebsite(http://www.broadinstitute. comparative genomics reveals the evolutionary relationships org/annotation/genome/fusarium_group/MultiHome. among toxin gene clusters whereby the loss and gain of genes html), which brought together high quality sequence from the cluster may be understood in an evolutionary context assemblies of the plant pathogenic fungus Fusarium grami- of toxin diversification. The genomic milieu of effector genes, nearum, sequenced previously [1] and two new WGS for encoding small secreted proteins, also suggests mechanisms the species Fusarium verticillioides and Fusarium oxysporum. that promote genetic diversification for the benefit of the At the sametime,theJoint Genome Institute (JGI) released pathogen. a WGS for Fusarium solani (Nectria haematococca)(http:// Addresses genome.jgi-psf.org/Necha2/Necha2.home.html). The four 1 Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of genomes share considerable sequence similarity as well as Science, University of Amsterdam, P.O. Box 94215, 1090 GE extensive synteny (Figure 1)[2,3]. Amsterdam, The Netherlands 2 USDA ARS Cereal Disease Laboratory, 1551 Lindig St., University of Minnesota, St. Paul, MN 55108, USA The Fusarium genomes consist of a core region with approximately 9000 genes considered to be orthologous Corresponding authors: Rep, Martijn ([email protected]) and Kistler, H Corby due to high sequence similarity and conserved gene order ([email protected]) [3]. Each species also contains thousands of genes that are unique to each genome, many of which are found near Current Opinion in Plant Biology 2010, 13:420–426 the ends of chromosomes. In F. graminearum, these tel- omere proximal regions are rich in gene diversity as This review comes from a themed issue on measured by SNP density [1] and are regions of elevated Biotic interactions Edited by Jane E. Parker and Jeffrey G. Ellis recombination [4]. Distinctively, F. graminearum also contains interstitial chromosomal regions of high diversity Available online 13th May 2010 and recombination that appear to have been created by an 1369-5266/$ – see front matter ancestral telomeric fusion of chromosomes [1 ,3 ]. How Published by Elsevier Ltd. these interstitial regions of F. graminearum chromosomes have maintained high genetic diversity, normally associ- DOI 10.1016/j.pbi.2010.04.004 ated with telomeres, remains a mystery. Comparative genomics with closely related Aspergillus Introduction species also has revealed large species-specific gene sets, Genomic sequencing of fungal phytopathogens has revo- which are concentrated in subgenomic regions called lutionized the study of plant pathogenesis. Whole gen- chromosomal islands [5 ]. Interestingly, these regions ome sequence (WGS) data for individual fungal genomes have a subtelomeric bias too. This could be due to the accelerated classical forward and reverse genetic inherent recombinogenic nature of chromosome ends but approaches for identifying pathogenicity genes. More seems to have functional implications as well; subtelo- recently, the availability of several WGS assemblies for meric gene expression is associated with invasive growth comparative genomic analysis has enabled unprece- of Aspergillus fumigatus in mammals and ex vivo neutrophil dented opportunities for tracing the evolutionary origin exposure [6]. (and demise) of genes and molecules that influence the outcome of fungal–plant interactions. Moreover, the over- Instead of genomic islands, both F. oxysporum and F. all genomic organization of fungal pathogenicity-related solani contain supernumerary chromosomes that largely genes has suggested novel modes of molecular diversifi- consist of lineage-specific sequences and make up a Current Opinion in Plant Biology 2010, 13:420–426 www.sciencedirect.com Genomic organization of plant pathogenicity in Fusarium species Rep and Kistler 421 Figure 1 Comparison of Fusarium Genomes. Synteny of the F. oxysporum, F. verticillioides, F. graminearum,andF. solani genomes determined by BLASTN alignment (cutoff 1e-10). Chromosomes (Chr) of F. oxysporum are used as a reference and the scale (bottom) measures chromosome size in megabases (Mb). Grey boxes indicate chromosome size determined by optical mapping, upon which are superimposed corresponding WGS assembly scaffolds displayed as numbered black bars. Unassembled scaffolds (Un) are concatenated for ease of display. Regions of shared gene order with chromosomes of F. verticillioides, F. graminearum and F. solani, are shown beneath each F. oxysporum chromosome. Sequences from individual chromosomes in each species are color-coded so that blocks of solid color represent regions of synteny with the F. oxysporum genome. Little homology or synteny is apparent for the lineage specific regions of F. oxysporum chromosomes 3, 6, 14 and 15 and for telomere-proximal portions of chromosomes 1 and 2. Figure modified from supplemental material of [3]. www.sciencedirect.com Current Opinion in Plant Biology 2010, 13:420–426 422 Biotic interactions substantial fraction of the entire genome [2,3]. Lin- co-cultivation, resulting in a new pathogenic lineage. eage-specific portions of F. oxysporum and F. solani are Lateral chromosome transfer, first observed in Colleto- highly enriched in transposable elements. Regions of high trichum gloeosporioides [17], likely explains the existence genome diversity in Fusarium, whether at chromosome of host-specific groups of strains ( formae speciales)ofF. ends, special interstitial sites or on supernumerary oxysporum composed of several independent lineages. chromosomes, also have been shown to be rich in genes This is supported by the observation that the sequences predicted to be involved in fungal–host interactions. High of the effector genes on the pathogenicity chromosome diversity regions are enriched for predicted secreted are, with few exceptions, identical between disparate proteins, carbohydrate-active enzymes and genes specifi- lineages and highly specific to lineages which are patho- cally expressed during plant infection [1,3,7]. genic to tomato [18]. Effector genes, pathogenicity chromosomes In the pea-pathogenic form of F. solani, supernumerary and horizontal transfer chromosomes also harbor genes for host-specific viru- Effectors are proteins secreted by pathogens that promote lence, including detoxification mechanisms and host virulence, commonly by interacting with plant host nutrient utilization [19,20]. Three supernumerary proteins [8]. Because of these interactions, effector genes chromosomes with sizes between 0.5 and 1.6 Mb have are frequently involved in molecular arms races between characteristics that distinguish them from the rest of the pathogen and plant and subject to accelerated evolution genome including higher levels of repeat sequences [9]. The location of effector genes in a genome may affect (mostly transposons), more duplicated and unique genes, the rate at which they evolve through mutation or recom- smaller average gene size and a lower G+C content. Like bination. In Leptosphaeria maculans, for instance, the in F. oxysporum, sequences of the genes on these chromo- effector (Avr) genes that have been identified through somes suggest activities consistent with habitat special- positional cloning all reside in AT-rich genomic subre- ization but no involvement in essential cellular functions gions of up to several hundred kb consisting mostly of [2]. For Alternaria alternata, too, host plant-specific remnants of retrotransposons [10,11,12]. These long pathogenicity can be attributed to supernumerary chromosomal segments of uniform AT/GC content are chromosomes, of 1.0–1.7 Mb [21]. Genes for synthesis similar to isochores found in other eukaryotes. of host-selective toxins that are crucial for host-specificity are located on these chromosomes [22]. Although these highly particular, isochore-like genomic subregions presently have been found only in L. maculans, Transposons the genomic location of effector genes is also non-random Could the proximity of effector genes to repeats or in several other fungi. In the corn pathogen Ustilago transposons accelerate their evolution? While Lepto- maydis, a significant fraction (18%) of the genes for sphaeria represents an extreme case of repetitive genomic secreted proteins are organized in 12 clusters (3–26 genes context of effector genes, the context of effector genes in per cluster) dispersed in the genome [13]. Most clusters other fungi is also often transposon rich [16,23]. In contain tandem arrays of 2–5
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